The church was founded in 1811 by Fr. John Baptist Pasqual, from Phuket in Thailand. Fr. Pasqual landed in Pulau Tikus and decided to build a church. Fr. Jacques-Honore Chastan, served as the fourth parish priest in the church from 1830-1833. He left for Korea to do his missionary work. He was persecuted by the Korean authorities for protecting the Korean Catholics. Pope John Paul II in 1984 canonised him. The original church building lasted until 1835 when it was replaced with a brick church. On the adjoining a boys' school, St. Xavier's Branch School and Pulau Tikus Convent was constructed nearby. In 1899, due to the collapse of one the ceilings in the church, it was rebuilt. The church survived until the late 1960s when it was further renovated until the facade today. Currently, the church serves about 5,000 Catholics residing around the north and north-east zone of Penang Island. The church is led by Fr Jude Miranda since October 2018 and assisted by Fr Francis Anthony. It also administers the Chapel of St. Joseph, located in Hong Seng Estate, Mount Erskine.